Shanghai | China has warned Australia not to target Beijing via its newly signed defence agreement with Japan and implied the pact could harm regional security.

In a curt response to the signing of the agreement in Canberra on Tuesday, China’s Foreign Ministry spokesman signalled Beijing’s displeasure.

“It is our hope that the co-operation between countries should make a positive contribution to regional peace and stability, not the opposite and not target a third party," said the spokesman Hong Lei.

The restrained but pointed response from Beijing highlights the difficult position the Abbott Government has made for itself.

In enhancing defence and security ties with Tokyo, its hopes of fostering greater economic co-operation with Beijing has become more difficult.

Canberra is hoping to sign a long awaited free trade agreement with Beijing by year’s end, which should provide greater access to the world’s second biggest economy for Australian farmers and service firms.

At this stage a deal still appears on track, but China has always said the main obstacles to the FTA were “political" not “economic".

Japanese Prime Minister Shinzo Abe is in Australia for a week long tour, following the visit of Prime Minister Tony Abbott to Tokyo in April.

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On Tuesday the pair singed a defence, science and technology agreement.

Mr Abe also became the first Japanese Prime Minister to address the Australian Parliament.

Abe rebukes China territorial claims

During his speech he did not directly single out China for criticism, but he made a number of pointed remarks about Beijing’s recent behaviour.

“We want to make Japan a country that will work to build an international order that upholds the rule of law," Mr Abe said in reference to China’s repeated refusal to be bound by international conventions or laws.

“Let us join together all the more in order to make vast seas from the Pacific Ocean to the Indian, and those skies, open and free," said Abe said in another pointed rebuke of China’s territorial claims and move last year to take control of air space claimed by Japan.

Sino-Japanese relations have deteriorated significantly over the last two years, as both sides increasingly harden their positions.

The renewed tensions were sparked by Japan’s mis-handling of a move to nationalise a string of disputed islands in the East China Sea.

Since then both sides have sharpened their rhetoric and adopted increasingly assertive military postures.

“The responsibility for the difficult relationship between China and Japan lies with Japan," said the Foreign Ministry spokesman on Tuesday.

His comments were in response to Mr Abe’s desire to hold talks with China in an effort to settle their differences.

“China has a very clear stand in improving and developing China-Japan relations," he said.

“We would like Japan to take concrete measures to remove political barriers to improve and develop the bilateral relationship."